It has been reported that there were seven mysteries that exist in the Fudo High School, though only six of them had been solved. The high school student Hajime Kindaichi is invited by the Mystery Research Team leader, Ruiko Sakuragi to help her solve the seventh riddle. There is even a possibility that if the old school building is demolished, a man called "After-School Magician" will begin to murder.

Ruiko has been killed in the locked biology classroom, and everyone in the school is worried. Makabe tells everybody his speculation about the trick and gives sarcasm to Kindaichi, yet another student manages to break out the code left by Ruiko as a dying message.

Miyuki gets heavily injured and is sent to hospital because of the attack from the killer and later wakes up. Kindaichi returns to the school in attempt to solve the mystery, therefore calling everybody inside to gather. The seventh mystery was man-made, and one man is said to be the murderer.

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「誰か来てくれ！金田一が逃げた！！」 「はじめちゃん・・・・・」 「自分の容疑はこの俺が自分で晴らしてやる！」 犯行現場の状況ははじめに不利なものばかりだった。話しを聞いてもらえず、橘 五柳殺人事件の容疑者として警察に連行されようとしたはじめは、自ら犯人を挙げる為に逃げ出した。 逃げるはじめ。追う警察。はじめを助けようとする美雪といつき達。事件を解く鍵は橘が出した暗号”裏川辺奇々なる藻を”と、新作の小説で暴かれるはずだった人物にある。暗号を解いたはじめは、ある人物に会いに行く。だがそこで新たなる惨劇が・・・・・剣持警部と明智警視が追手に加わり、次第に追いつめられていくはじめ。 このまま真犯人の策略にはまってしまうのか？ 「絶対に許さない！正体を暴いてやる。ジッチャンの名にかけて！！」

「きゃーっ！人殺しー！！」 「くそっ、これじゃ俺は連続殺人鬼だぜ」 「リターンマッチです。彼が逃げるか、私（明智）が捕えるかのね」 暗号は、人から人へとつながっている最初のキーだった。 その伝言役になっていた大村、時任、桂の三人が殺された。そしてその全ての現場にいたはじめは、連続殺人犯として手配されてしまったのだった。桂が指定した次の人物、野中に会いに軽井沢に向かうはじめだが、電車の中で警察に包囲されてしまう。決死の覚悟で逃げおおせたはじめだったが、目的地のホテルには既に明智をはじめとする警察の方位網が敷かれていたのだった。ついにはじめは捕まってしまうのか？ ビデオや写真に謎は隠されているのか？？ 真犯人はどうやって足跡を残さずに逃げれたのか？？？

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A famous writer recently died and according to his will, his inheritance will be divided by his five successors. One of the successors, Takarada invites Hajime, Saki and Miyuki to the Russian Mansion in Hokkaido.

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